Hi,
Yes presets should not dissapear from the preset folder, if you have saved presets. But as with all things on computers, then it's a good idea to create backups of your files, in case anything go wrong.
If you don't create backups of your files allready, then i recommend, you begin to do that.
As you mention V-Collection, then i can add, that you in example get Jup-4 V. Jup-3 V presets can't be used in Jup-4 V, but Jup-4 install alongside Jup-3 V.
I can't tell, if there are bugs - also when used in hosts. Keep an eye on the forum.